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simulation of the TIP3P water box. RISM calculations were performed in two steps. At first, standard RISM calculations with KH closure were performed at 300 K with water density of 55.5 M and NaCl ...
conformation, for which we obtained atomic coordinates from the ambertools software package (http://casegroup.rutgers.edu/). Simulations were performed with the Amber03 force-field (43) and the TIP3P water model ...
– Simulated system Abbreviation Run length (μs) No. of equivalent runsb Cumulative time (μs) No. of strands Ions 1 2M18 dimer 2M18-D 10 3 30 4 NaCl 2 2M18 monomer 2M18-M 10 6 60 2 NaCl 3 2M18 hairpin 2M18-H 1 8 ...
of experimental observables and their computational analogues NMR spectroscopy [63] has previously confirmed the intrinsic disorder of the prodomain. Many of the common force-field and water model combinations used ...
-grained simulations . Residue-based coarse-grained simulations are performed using the MARTINI force field, version v2.2P, with the MARTINI polarizable water model [67, 68]. In the MARTINI model, each amino ...
against 5-LOX and determine their structure-function mechanism through virtual screening, molecular docking, and molecular dynamics simulation . The results of our computational study would provide ...
– 1958 . Google Scholar PubMed 39. Smith D.E. , Dang L.X. Computer simulations of NaCl association in polarizable water . J. Chem. Phys. 1994 ; 100 : 3757 – 3766 . Google Scholar Crossref Search ADS 40 ...
by contemporary computational chemistry tools is entirely inaccessible due to the fundamental disparity between the simulation time-scales and the time-scale of the real folding processes (58). Thus, while ...
) and (compound A02), using a combination of in vitro assays, computational methods, and molecular simulations . Both compounds were evaluated for their impact on cancer cell lines and DNA binding capacity utilizing ...
. Simulations meet experiment to reveal new insights into DNA intrinsic mechanics . PLOS Comput . Biol. 2015 ; 11 : e1004631 . Google Scholar Crossref Search ADS PubMed 16. Tian Y. , Kayatta M. , Shultis K ...
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